22-39343633-C-G

Variant names:

• chr22-39343633-C-G
• rs137686

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.774 in 152,004 control chromosomes in the GnomAD database, including 45,692 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.77 (45692 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117549 AN: 151886 Hom.: 45660 Cov.: 32

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.755

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.774 AC: 117636 AN: 152004 Hom.: 45692 Cov.: 32 AF XY: 0.775 AC XY: 57543 AN XY: 74292

African (AFR) AF: 0.813 AC: 33720 AN: 41490

American (AMR) AF: 0.824 AC: 12559 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2592 AN: 3472

East Asian (EAS) AF: 0.864 AC: 4470 AN: 5176

South Asian (SAS) AF: 0.855 AC: 4121 AN: 4822

European-Finnish (FIN) AF: 0.711 AC: 7493 AN: 10544

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50318 AN: 67936

Other (OTH) AF: 0.754 AC: 1593 AN: 2114

Alfa AF: 0.637 Hom.: 1772

Bravo AF: 0.781

Asia WGS AF: 0.820 AC: 2850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.37
PhyloP100		-0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs137686; hg19: chr22-39739638;